tag:blogger.com,1999:blog-7549031172158127172.post1803257467531901753..comments2014-06-14T06:40:54.862-07:00Comments on Internship Systems Biology solutions to Malaria: Week 4 (14-18 May 2014)Patricia Zaandamhttp://www.blogger.com/profile/16390816251887310513noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-7549031172158127172.post-73789567189664355642014-05-28T02:34:47.323-07:002014-05-28T02:34:47.323-07:00I was also wondering why you describe the wanted m...I was also wondering why you describe the wanted minimal Fold Change as: | logFC | >0.585 , what you really mean is a real change of 50% up or down, right? Did you try lower values? In large processes many small changes actually can make sense.Chris Evelohttps://www.blogger.com/profile/17224981213656983957noreply@blogger.comtag:blogger.com,1999:blog-7549031172158127172.post-27735061757939778622014-05-28T02:28:25.039-07:002014-05-28T02:28:25.039-07:00Please do put in links to actual data loaded pathw...Please do put in links to actual data loaded pathways. We do say "never publish a list like this" during courses on pathway analysis for a reason. I understand that for blog posts you can post the list as part of an ongoing process, but the next step really is to look at the pathways themselves. Pathway statistics often does not make a lot of sense on its own. I can give you some reasons for that. Adding a bunch of non regulated genes to pathway for instance lowers its ranking without changing the biology, some pathways highly overlap and they may all show up for that reason while that points to only one sub process really. Also some individual steps in metabolism or regulation can often be done by different genes. Now having one active and differently regulated gene in one step where actually 10 could be active is not necessarily less relevant than having 1 out of 1 for the next one. Having 2 out of 10 could be less meaningful if the next step is not regulated at all. These lists thus are *just* a link to a further interpretation of the outcome.Chris Evelohttps://www.blogger.com/profile/17224981213656983957noreply@blogger.com